.. _scripts:

Scripts
=======

**pmx** provides a few command line scripts that can be used to setup and analyse
free energy calculations. After installing the library, ``pmx``
should be in your  ``$PATH``. You can check this with the following command. ::

  $ which pmx

The ``pmx`` help will show the scripts available. ::

   $ pmx -h
   usage: pmx [-h]

    ------------------------
    pmx command line scripts
    ------------------------

    Available commands are:
        mutate       Mutate protein or DNA/RNA
        gentop       Fill hybrid topology with B states
        analyse      Estimate free energy from Gromacs xvg files

        doublebox    Place two input structures into a single box
        abfe         Setup files for an ABFE calculation

        genlib       Generate pmx ff library
        gmxlib       Show/set GMXLIB path

    optional arguments:
        -h, --help  show this help message and exit

A description of these scripts can be found here:

.. toctree::
   :maxdepth: 1

   mutate
   gentop
   analysis
   genlib

In the :ref:`examples` you can find instead how the same tasks can be carried out
using the API.